[phenixbb] CASP 10: Call for targets to assess the state of the art in protein structure modeling
torsten.schwede at unibas.ch
Fri May 11 06:24:38 PDT 2012
*CASP 10: Call for targets to assess the state of the art in protein
As many of you know, CASP (Critical Assessment of Structure prediction)
has been assessing the state of the art in modeling protein structure
from sequence since 1994, running a community experiment once every two
years. In these experiments, information on soon to be solved structures
is collected from the experimental community, and the sequence data are
passed to the structure modeling community so that blind predictions of
structure and can collected and assessed (1). Over that period CASP has
seen enormous progress in the quality of modeled structures (2), but
many problems remain. CASP is only possible because of the generous
participation of the experimental community in providing the modeling
targets (3). We recently appealed for your help in providing novel fold
and membrane protein targets for the ongoing CASP ROLL process. That is
very successful, with 57 prediction teams participating and 26 targets
already released, thanks to all of you who have contributed.
The prediction season for the next full biannual experiment, CASP 10,
begins May 1, and so we are now asking for your help again, this time in
reaching our goal of releasing at least varied 100 targets in a the
three-month period. We need all sorts of targets, spanning the
1. (More than ever) novel folds and membrane protein targets -- even
with the extended collection season provided by CASP ROLL, there will be
still a shortage. There are some interesting methods developments for ab
initio modeling, and it is important to be able to decisively evaluate
2. A diversity of comparative modeling targets. Cases where the there is
fairly high sequence identity (30-50%) between the target structure and
an available template are valuable for testing the degree to which model
accuracy can approach that of experiment, particularly in functionally
critical regions. Cases with lower sequence identity to template, right
down to undetectable, are valuable for testing the ability of the
methods to detect remote homologs, to overcome challenging alignment
difficulties, to make use of multiple templates, and to build regions of
the structure not obviously available from a template.
3. Targets containing significant amounts of disordered structure, so as
to test the ability of methods to identify these regions. Disorder
identified by absence of density in crystallography is current the main
source and very useful, but its important to have cases where the nature
of the disorder has been established by other means, such as NMR.
4. Some targets will also be used to test methods of structure
refinement. In these cases, the best model received for a target will be
released to the refinement community, who will subsequently submit new
models. This too is an area where there have been some exciting
developments in the last year, so we are hoping for significant
progress. Refinement targets are selected based on the nature of the
errors in the initial models. Because of the extended process, these
targets need to be available for longer before release of the
For those of you who have not provided targets to CASP before, the
procedure is simple. There are three ways to submit targets: (1) Go the
target submission web page and fill in the easy form; (2) When you
submit your co-ordinates to the PDB, tick the 'CASP HOLD' box,
automatically setting up a target entry; (3) Send an email the
prediction center with details. If you have queries, there is a very
experienced prediction center staff to deal with them. The key thing is
timing: We need a window of at least four weeks between receiving
information about a target and the release of your experimental
structure. A longer window -- up to eight weeks - is often useful, for
example so that a target can be used to test refinement methods, but is
not essential (note that using the PDB target submission route
automatically selects eight weeks). We don't need your experimental
structure in advance of its release by the PDB, provided that will
happen by the end of August. Please consult the target submission page
for more details:
There are already over 200 prediction teams signed for CASP 10, and so
any targets provided will receive plenty of attention. If you have a
suitable target now, we are ready to receive it. If new targets come up
before July 17, we would also love to have them. (After July 17, we will
continue with CASP ROLL for novel folds and membrane proteins). So
please get in touch whenever a suitable opportunity arises, and help
improve modeling methods.
CASP organizing committee
John Moult, IBBR, University of Maryland, USA
Krzysztof Fidelis, University of California, Davis, USA
Andriy Kryshtafovych, University of California, Davis, USA
Torsten Schwede, SIB & Biozentrum University of Basel, Switzerland
Anna Tramontano, University of Rome, Italy
Get in touch: casp at predictioncenter.org
More information: http://www.predictioncenter.org/casp10/index.cgi
CASP Roll targets so far:
Submit a target:
1. Critical assessment of methods of protein structure prediction
(CASP)--round IX. <http://www.ncbi.nlm.nih.gov/pubmed/21997831>
Moult J, Fidelis K, Kryshtafovych A, Tramontano A.
Proteins. 2011;79 Suppl 10:1-5. doi: 10.1002/prot.23200. Epub 2011 Oct 14.
2. CASP9 results compared to those of previous CASP experiments.
Kryshtafovych A, Fidelis K, Moult J.
Proteins. 2011;79 Suppl 10:196-207. doi: 10.1002/prot.23182. Epub 2011
3.Target highlights in CASP9: Experimental target structures for the
critical assessment of techniques for protein structure prediction.
Kryshtafovych A et al.
Proteins 2011;79 Suppl 10:6-20. doi: 10.1002/prot.23196. Epub 2011 Oct 21.
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the phenixbb